The 44-year-old also intimated that the Argentine would have made an appearance had he believed his side still had a chance of progressing
The Argentine attacker was a surprise omission from the Blaugrana starting line-up against the Bavarians, with many speculating that he suffered a recurrence of his recent hamstring knock prior to the 3-0 defeat.
However, this was not the case according to his coach, who also claimed that Messi would have made an appearance in the second half had he thought the Catalans still had a chance of making the final on May 25.
"Messi was not injured, but he was not feeling okay, and I thought that in his situation he would not help the team," Vilanova told reporters.
"He played in Bilbao because he was in much better condition, but at the end of the game he contracted some strange sensations.
"We would have taken the risk of playing Leo towards the end of the match if we still had a chance of making the final."
Reflecting on his side's performance at Camp Nou, Vilanova admitted that Barca were "massively" outclassed by Bayern but insisted that widespread personnel changes would not be necessary during the close season.
"Bayern are physically at a great level. The difference today between the sides was massive and I congratulate them on their progression, but also thanks to our fans for their support," he added.
"We've been suffering with injuries all season and at this level you pay for that. Every squad needs to be changed, but we have a good squad already.
"We don't need to make a lot of changes as we have some players who are still recovering."
Meanwhile, David Villa supported Vilanova's assertion that Messi was not in the right physical condition to start at Camp Nou, but nonetheless urged his team-mates to move on quickly from their European humbling.
"They were better during both matches, we must admit it. We're sad because we were close to Wembley but they deserved it and we must congratulate them," the Spain striker remarked.
"We tried to attack from the beginning in order to quickly reduce the aggregate, but the difference was too big in the end.
"Messi wanted to play but during the day he knew he wouldn't be able to do it. It's not an excuse, even if he is the best player in the world.
"Now we must forget about the Champions League and focus on La Liga. There are still many happy moments that we are yet to experience and we are close to winning the league title."